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147     <td><font size=5>PyMsXML</font></td>
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158    
159     <!-- CONTENT STARTS HERE -->
160    
161     <h3>Introduction</h3>
162     <P>
163     <b>PyMsXML</b> is a python script for converting vendor specific mass
164     spectrometry data files for Applied Biosystems' Q-Star, 4700, Mariner,
165     and Voyager mass spectrometers from their raw binary form, to either
166     of the emerging XML file formats for mass spectra: mzXML, from the
167     Sashimi Glossolalia project of the Institute for Systems Biology (ISB);
168     and mzData, from the Proteome Standardization Initiative (PSI) project
169     of the Human Proteome Organization (HUPO).
170     <P>
171     <b>PyMsXML</b> uses installed vendor software under Windows to access the
172     proprietary raw mass spectra file format, interfacing to the vendor
173     supplied libraries via the supplied COM interface. Unlike other
174     software solutions that use this approach, <b>PyMsXML</b> is written in a
175     free, open-source language called Python. As such, no installation of
176     Microsoft Visual C++ or Visual Basic is necessary to use, alter, or
177     improve the <b>PyMsXML</b> script.
178     <P>
179     <b>PyMsXML</b> is easily extended for new instruments and vendor software,
180     and for new, or changed, XML file formats. The code that interfaces to
181     the vendor software is decomposed from the code that formats the data
182     as XML, as such, the addition of new instrument capability need not
183     re-write the XML data format code. Similarly, as new XML file formats
184     emerge, the code that interfaces with the instrument software need not
185     change.
186     <P>
187     <h3>Installation</h3>
188     <P>
189     <ol>
190     <li> Download and install the latest version of <A href="http://www.activestate.com/Products/ActivePython/">ActiveState ActivePython</A> for Windows.
191     <P>
192     <li> Start the Pythonwin IDE (All Programs -> ActiveState ActivePython
193     2.4 -> Pythonwin IDE). From the Tools menu, select the "COM Makepy
194     utility" entry. In the popup window, select "ExploreDataObjects 1.0
195     Type Library (1.0)" to build a python interface to Analyst's COM
196     libraries for reading .wiff files, select "IDAExplorer 1.0 Type
197     Library (1.0)" to build a python interface to Data Explorer's COM
198     libraries for reading ".dat" and ".t2d" files. If you have both pieces
199     of software, repeat this step for each software package. Click OK.
200     <P>
201 nje01 1.2 <li> Check the installation of COM library interfaces. If any of these
202     tests are unsuccessful, then <b>PyMsXML</b> will be unable to read the
203     corresponding raw datafiles.
204 nje01 1.1 <P>
205 nje01 1.2 For Analyst, these commands at the Pythonwin IDE command-line
206     (copy-and-paste!) should elicit similar responses:<br>
207 nje01 1.1 <code>
208     >>> from win32com.client import Dispatch<br>
209     >>> Dispatch('Analyst.FMANSpecData')<br>
210     &lt;win32com.gen_py.ExploreDataObjects 1.0 Type Library.IFMANSpecData instance at 0x14421558> <br>
211     >>> Dispatch('Analyst.FMANChromData')<br>
212     &lt;win32com.gen_py.ExploreDataObjects 1.0 Type Library.IFMANChromData instance at 0x14418408>
213     </code>
214     <P>
215     For Data Explorer, these commands at the Pythonwin IDE command-line (copy-and-paste!) should elicit similar responses:<br>
216     <code>
217     >>> from win32com.client import Dispatch, gencache<br>
218     >>> Dispatch('DataExplorer.Application',resultCLSID='{3FED40F1-D409-11D1-8B56-0060971CB54B}')<br>
219     &lt;COMObject DataExplorer.Application><br>
220     >>> gencache.EnsureModule('{06972F50-13F6-11D3-A5CB-0060971CB54B}',0,4,2)<br>
221     &lt;module 'win32com.gen_py.06972F50-13F6-11D3-A5CB-0060971CB54Bx0x4x2' from 'C:\Python24\lib\site-packages\win32com\gen_py \06972F50-13F6-11D3-A5CB-0060971CB54Bx0x4x2.py'>
222     </code>
223     <P>
224     <li> Download and unpack the <b>PyMsXML</b> scripts and examples. <A
225 nje01 1.3 href="http://bioinformatics.org/project/filelist.php?group_id=701">Download
226 nje01 1.1 <b>PyMsXML</b></A>. After unzipping <b>PyMsXML</b>, edit the file pymsxml.cmd to
227     point to your Python installation (usually C:\Python24\python.exe)
228     and your <b>PyMsXML</b> installation.
229     </ol>
230     <P>
231     <h3>Usage</h3>
232     <P>
233     <b>PyMsXML</b> consists of a single python script. A windows cmd file wrapper is provided, to take care of calling the python interpretor appropriately.
234     <dl>
235     <dt><b>pymsxml</b> [ options ] <i>raw-spectra-data-file</i></dt>
236     <P>
237     <dt>
238     Options:<P>
239     </dt>
240     <dd>
241     <dl>
242     <dt>-R <i>raw-format</i>, --rawdata <i>raw-format</i></dt>
243 nje01 1.2 <dd>Valid <i>raw-format</i> values: <tt>wiff</tt>, <tt>qstar</tt>, <tt>t2d</tt>, <tt>ab4700</tt>, <tt>voyager</tt>, <tt>mariner</tt>, <tt>mzXML</tt>. Optional if <i>raw-spectra-data-file</i> ends in <tt>.wiff</tt>, <tt>.t2m</tt>, or <tt>.mzXML</tt>.
244 nje01 1.1 <P>
245     <dt>-X <i>xml-format</i>, --xmlformat <i>xml-format</i></dt>
246     <dd>Valid <i>xml-format</i> values: <tt>mzXML</tt> (ISB), <tt>mzData</tt> (HUPO). Optional if <i>output-file</i> ends in <tt>.mzXML</tt> or <tt>.mzData</TT>.
247     <P>
248     <dt>-o <i>output-file</i>, --output <i>output-file</i></dt>
249     <dd>Name of output file. If omitted, and <i>xml-format</i> is supplied, then the output file is inferred by changing the file extention of <i>raw-spectra-data-file</i> to <i>xml-format</i>.
250     <P>
251     <dt>-p <i>ms-levels</i>, --peaks <i>ms-levels</i></dt>
252     <dd> Apply (vendor library) peak detetion to spectra with level in <i>ms-levels</i> (comma separated). QStar (MS/MS spectra only) raw format, 4700 raw format only. Default: 2.
253     <P>
254 nje01 1.2 <dt>-f <i>filter-spec</i>, --filter <i>filter-spec</i></dt> <dd>
255     Filter output scans by their meta-data. Filters are specified as a
256     comma-separated list of filter tokens. Each filter token is specified
257     as <i>field</i>.<i>comparison</i>.<i>value</i>. <i>field</i> must be
258     an attribute of the scan object. <i>comparison</i> must be one of
259     <tt>eq</tt>, <tt>ne</tt>, <tt>lt</tt>, <tt>le</tt>, <tt>gt</tt>, or
260     <tt>ge</tt>, specifying =, &ne;, &lt;, &le;, &gt;, and &ge;
261     respectively.
262 nje01 1.1 <P>
263     <dt>-Z <i>compress-format</i>, --compress <i>compress-format</i></dt>
264 nje01 1.2 <dd> Compress output file. Valid options: <tt>gz</tt>. Default: None, unless output file ends with <tt>.gz</tt>, then <tt>gz</tt>.
265 nje01 1.1 <P>
266     <dt>-d, --debug</dt>
267     <dd>Debug. Output XML for first 10 spectra only. Truncate spectral data, too. Useful to verify that the output is formatted correctly.</dd>
268     <P>
269     <dt>-h, --help</dt>
270     <dd>Help.</dd>
271     </dl>
272     </dd>
273     </dl>
274     <P>
275     <h3>Applied Biosystems Q-Star Spectra</h3>
276     <P>
277     The raw spectra data files for the ESI spectra from Applied
278 nje01 1.2 Biosystems' Q-Star instruments are usually extracted as ".wiff"
279     files. These can be opened using Applied Biosystem's Analyst or
280     BioAnalyst programs. <b>PyMsXML</b> uses Analyst's support libraries
281     to extract mass spectra from these files.
282 nje01 1.1 <P>
283     <P>
284     <h3>Applied Biosystems Mariner, Voyager, 4700 Spectra</h3>
285     <P>
286     The raw spectra data files for the MALDI spectra from Applied
287     Biosystems' Mariner, Voyager and 4700 instruments are usually
288     extracted as ".t2d" or ".dat" files. These can be opened using Applied
289     Biosystem's Data Explorer program. <b>PyMsXML</b> uses Data Explorer's
290 nje01 1.2 support libraries to extract mass spectra from these
291 nje01 1.1 files. These file formats store very little meta-data in addition to
292     the mass spectrum. As such, additional information must be supplied in
293     a meta-data text file, which is supplied on the command-line as <i>raw-spectra-data-file</i>.
294     <P>
295     The meta-data file is most easily constructed in Excel and saved as
296     tab-separated-values, but it can be formed by hand too, if
297     desired. Each line of the meta-data file specifies a record,
298     describing the MALDI plate, the plates' spots, and the scans acquired
299     from these spots. A short-cut record, that defines the plate and spot
300     naming convention is also provided.
301     <P>
302     The plate definition record consists of the word <tt>PLATE</tt> (case
303     insensitive) in the first column, followed by alternating key-value
304     pairs in subsequent columns. Particular key-value pairs do not need to
305     be specified in any particular order. The following keys must be
306     provided:
307     <tt>plateID</tt>, <tt>spotXCount</tt>, <tt>spotYCount</tt>,
308     <tt>plateManufacturer</tt>, and <tt>plateModel</tt>. The
309     <tt>plateID</tt> value is referenced by the spot and scan definition
310     records. The <tt>spotXCount</tt> is the number of MALDI spots in
311     the horizontal dimension (integer). The <tt>spotYCount</tt> is
312     the number of MALDI spots in the vertical dimension (integer). The
313     <tt>plateManufacturer</tt> and <tt>plateModel</tt> values are inserted verbatim in the output XML.
314     <P>
315     The spot definition record consists of the word <tt>SPOT</tt> (case
316     insensitive) in the first column, followed by alternating key-value
317     pairs in subsequent columns. Particular key-value pairs do not need to
318     be specified in any particular order. The following keys must be
319     provided:
320     <tt>plateID</tt>, <tt>spotID</tt>, <tt>spotXPosition</tt>,
321     <tt>spotYPosition</tt>, and <tt>maldiMatrix</tt>. The
322     <tt>plateID</tt> value must be defined by some plate definition
323     record. The <tt>spotID</tt> is referenced by the scan definition
324     records. The <tt>spotXPosition</tt> is the horizontal position of the
325     spot on the plate (integer). The <tt>spotYPosition</tt> is the
326     vertical position of the spot on the plate (integer). Spot positions
327     can be numbered beginning at 0 or 1. The
328     <tt>maldiMatrix</tt> value is inserted verbatim in the output XML.
329     <P>
330     The scan definition record consists of the word <tt>SCAN</tt> (case
331     insensitive) in the first column, followed by alternating key-value
332     pairs in subsequent columns. Particular key-value pairs do not need to
333     be specified in any particular order. The following keys must be
334     provided:
335     <tt>plateID</tt>, <tt>spotID</tt>, <tt>filename</tt>, and <tt>index</tt>.
336     The
337     <tt>plateID</tt> must be defined by some plate definition record. The
338     <tt>spotID</tt> must be defined by some spot definition record. The
339     <tt>filename</tt> is the name of the ".dat" or ".t2d" file containing
340     the corresponding scan's spectrum. The <tt>index</tt> is the ordinal
341     of the corresponding spectrum in the provided file. Spectra within
342     files should be referenced beginning at 1.
343     <P>
344     To alleviate some of the tedium with specifying the spot definition records, a shortcut plate definition record is provided. The platedef definition record consists of the word <tt>PLATEDEF</tt> (case insensitive) in the first column, followed by alternating key-value
345     pairs in subsequent columns. Particular key-value pairs do not need to
346     be specified in any particular order. The following keys must be
347     provided:
348     <tt>plateID</tt>, <tt>plateManufacturer</tt>, <tt>plateModel</tt>, <tt>spotNaming</tt>, and <tt>maldiMatrix</tt>.
349     The
350     <tt>plateID</tt> value is referenced by the spot and scan definition
351     records. The <tt>plateManufacturer</tt> and <tt>plateModel</tt> are
352     used to identify the properties of the MALDI plate. Currently, only
353     the values <tt>ABI / SCIEX</tt> and <tt>01-192+06-BB</tt> are
354     recognized, but others are easily added on request. The "ABI / SCIEX
355     01-192+06-BB" plate consists of 8 rows of 24 spots (plus 6 calibration
356     spots). The <tt>spotNaming</tt> must be one of <tt>alpha</tt>,
357     <tt>parallel</tt>, or <tt>antiparallel</tt>. At this time, only
358     <tt>alpha</tt> is implemented. The <tt>alpha</tt> spot attribute
359     constructs <tt>spotID</tt> values for all spots on the plate with the
360     row specified by a letter from A to H, and the column specified by a
361     number from 1 to 24. The
362     <tt>maldiMatrix</tt> value is assumed the same for each spot and is
363     inserted verbatim in the output XML.
364     <P>
365     <b>NOTE:</b> The order of scan definition lines is important! MS/MS
366     spectra must appear immediately after the MS spectrum containing their
367     precursors.
368     <P>
369     Example meta-data files are provided in the distribution. <tt>example1.t2m</tt> explicitly defines the MALDI plate, spots and scans. <tt>example2.t2m</tt> is equivalent, but uses the platedef keyword shortcut.
370     <P>
371     <h3>Examples</h3>
372     <P>
373     Convert the Q-Star <tt>example.wiff</tt> file to mzXML format, placing the output in the file <tt>qstar-example.xml</tt>.<P>
374     <code>
375     C:\PyMsXML\example\wiff> pymsxml.cmd -R wiff -X mzXML -o qstar-example.xml example.wiff<br>
376     </code>
377     <P>
378     Convert the Q-Star <tt>example.wiff</tt> file to mzData format, placing the output in the file <tt>example.mzData</tt>.<P>
379     <code>
380     C:\PyMsXML\example\wiff> pymsxml.cmd -X mzData example.wiff<br>
381     </code>
382     <P>
383     Convert the AB4700 spectra listed in <tt>example1.t2m</tt> and <tt>example2.t2m</tt> to mzXML format, placing the output in the files <tt>example1.mzXML</tt> and <tt>example2.mzXML</tt>.<P>
384     <code>
385     C:\PyMsXML\example\t2d> pymsxml.cmd -X mzXML example*.t2m<br>
386     </code>
387     <P>
388     <h3>Release Notes</h3>
389     <P>
390     The Analyst COM libraries seem to have trouble with long pathnames. If you consistently have trouble getting PyMsXML to read ".wiff" files, try moving the files to a shorter directory path.
391     <P>
392     <h3>Credits</h3>
393     <P>
394     Development of <b>PyMsXML</b> was significantly helped by the
395     open-source Visual Basic source code from the MzStar program of the
396     ISB glossolalia project.
397     <P>
398     <!-- CONTENT ENDS HERE -->
399     </td>
400     </tr>
401     </table></td>
402     <td bgcolor="#FFFFFF" width=10 valign="top"><img src="../images/top_shadow.gif" width=10 height=10></td>
403     </tr>
404     <tr>
405     <td bgcolor="#FFC621" width=120 colspan=3><img src="../images/blank.gif" width=10 height=1></td>
406     <td bgcolor="#FFFFFF" width=10 valign="top" background="../images/left_shadow.gif"><table border=0 cellspacing=0 cellpadding=0 background="../images/left_shadow.gif" width="10">
407     <tr>
408     <td valign="top"<img src="../images/left_shadow.gif" width=10 height=50></td>
409     </tr>
410     </table></td>
411     <td bgcolor="#FFFFFF" align="center">
412    
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443     Original created by <a href="mailto:jfuetsch@umiacs.umd.edu">John Fuetsch</a><br>
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